Thousands of genome-wide association studies (GWAS) have been conducted to identify the genetic variants associated with complex disorders. However, only a small proportion of phenotypic variances can be explained by the reported variants. Moreover, many GWAS failed to identify genetic variants associated with disorders displaying hereditary features. The “missing heritability” problem can be partly explained by rare variants. We simulated a causality scenario that gestational ages, a quantitative trait that can distinguish preterm (<37 weeks) and term births, were significantly correlated with the rare variant aggregations at 1000 single-nucleotide polymorphism loci. These 1000 simulated causal rare variants were embedded into randomly selected subsets of 9642 promoter regions from the 1000 Genomes Project genotypic data according to different proportions of causal rare variants within the embedded promoters. Through analysis of the correlations between rare variant aggregations and gestational ages, we found that the embedded promoters as a whole showed weaker genetic association when the proportion of causal rare variants decreased, and no individual embedded promoters showed genetic association when the proportion of causal rare variants was smaller than 0.4. Our analyses indicate that association signals can be greatly diluted when causal rare variants are dispersedly and sparsely distributed in the genome, accounting for an important source of missing heritability.